As part of the National Water Census program in the Apalachicola-Chattahoochee-Flint (ACF) River Basin, the U.S. Geological Survey evaluated the groundwater budget of the lower ACF, with particular emphasis on recharge, characterizing the spatial and temporal relation between surface water and groundwater, and groundwater pumping. To evaluate the hydrologic budget of the lower ACF River Basin, a groundwater-flow model, constructed using MODFLOW-2005, was developed for the Upper Floridan aquifer and overlying semiconfining unit for 2008–12. Model input included temporally and spatially variable specified recharge, estimated using a preliminary version of a Precipitation-Runoff Modeling System (PRMS) model for the ACF River Basin, and pumping, partly estimated on the basis of measured agricultural pumping rates in Georgia. The model was calibrated to measured groundwater levels, and base flows which were estimated using hydrograph separation. The simulated groundwater flow budget resulted in a net cumulative loss in groundwater storage during the study period. Spatial variability in simulated hydrologic budgets for eight subbasins was attributed to such factors as soil storage capacity, Lake Seminole impoundment, and the presence of in-channel springs. The model simulated a net storage loss for all the subbasins. The model is limited by its conceptualization, the data used to represent and calibrate the model, and the mathematical representation of the system; therefore, any interpretations should be considered in light of these limitations. In spite of these limitations, the model provides insight regarding water availability in the lower ACF River Basin. This USGS data release contains all of the input and output files for the simulations described in the associated model documentation report (https://doi.org/10.3133/sir20175141).